1) When a basestar is destroyed, is it also removed from the game like when a viper or civ ship is destroyed?  Personally I would think not, since the base game is limited to only 2 basestar tokens. It would be too easy for the humans to destroy them and not have to worry any more about them.

2) Can unrevealed cylons attack friendly ships?  i.e. Can they pilot a viper and attack civ's, other vipers or Galactica?  What about if the Admiral is an unrevealed cylon, can they nuke Pegasus or other ships?

3) When sending someone to the Brig (via the Admiral's qts or with the President) what happens if that person is on Colonial 1?  Do they still just automatically move to the Brig, or are they immune?

4) Are the token limitations to the base game unchangeable?  If I wanted to create several more basestar tokens so that when multiple crisis cards indicate more basestars, can I play them (the same would be if I got the expansions that give more tokens)?  What about with the basestar damage tokens?  Having only 4 seems a little short.  While it logistically works with only 2 basestars on the board (2 tokens each, so a 3rd damage would remove the basestar and the damage tokens return to the pool) it seems silly that you can't have hangar bay damage to both basestars, that you're limited to only one type of damage per basestar.

TIA!

1) No.  They can come back over and over.

2) No to all your examples; nukes must target basestars only (in the Exodux expansion they have a chance of destroying all ships in a space, and thus any humans also present), they cannot use vipers on ships or use Galactica to shoot ships; Pegasus expansion allows for Pegasus to hit human ships "by accident" (low rolls of dice).  Unrevealed cylons can make other decisions, such as on cards, that lead to destroying ships.

3) People can move to the brig from anywhere except the cylon locations, New Caprica, and the brig (i.e., they can't be chosen if they are already there).

4) Yes, the limit is unchangeable.